Commercial roof and drain gutter repair

I have a commercial building with comp. shingles shedding onto a sheet metal gutter on both sides of the 4/12 pitch roof. The metal gutter has corroded through the years due to water ponding segments. I have patched the metal gaps with mastic from time to time. Now, the corrosion is rusting through the metal gutter in pinpoint openings too small to detect or see with normal visual inspections causing leakage into the shop space underneath. I am considering hot mopping the metal valley gutter drain but am concerned that the added asphalt layering will thwart a positive water flow, exacerbate water ponding sections, and stifle drainage down to the end downspouts. Any ideas? Your input is much appreciated! Thanks.